!
@abstract Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF)
or possibly-compressed textual line-orientated file
@param fn The file name or "-" for stdin/stdout. For indexed files
with a non-standard naming, the file name can include the
name of the index file delimited with HTS_IDX_DELIM
@param mode Mode matching / rwa[bceguxz0-9]* /
@discussion
With 'r' opens for reading; any further format mode letters are ignored
as the format is detected by checking the first few bytes or BGZF blocks
of the file. With 'w' or 'a' opens for writing or appending, with format
specifier letters:
b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)
c CRAM format
g gzip compressed
u uncompressed
z bgzf compressed
[0-9] zlib compression level
and with non-format option letters (for any of 'r'/'w'/'a'):
e close the file on exec(2) (opens with O_CLOEXEC, where supported)
x create the file exclusively (opens with O_EXCL, where supported)
Note that there is a distinction between 'u' and '0': the first yields
plain uncompressed output whereas the latter outputs uncompressed data
wrapped in the zlib format.
@example
rwb .. compressed BCF, BAM, FAI
rwbu .. uncompressed BCF
rwz .. compressed VCF
rw .. uncompressed VCF
! @abstract Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF) or possibly-compressed textual line-orientated file @param fn The file name or "-" for stdin/stdout. For indexed files with a non-standard naming, the file name can include the name of the index file delimited with HTS_IDX_DELIM @param mode Mode matching / rwa[bceguxz0-9]* / @discussion With 'r' opens for reading; any further format mode letters are ignored as the format is detected by checking the first few bytes or BGZF blocks of the file. With 'w' or 'a' opens for writing or appending, with format specifier letters: b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc) c CRAM format g gzip compressed u uncompressed z bgzf compressed [0-9] zlib compression level and with non-format option letters (for any of 'r'/'w'/'a'): e close the file on exec(2) (opens with O_CLOEXEC, where supported) x create the file exclusively (opens with O_EXCL, where supported) Note that there is a distinction between 'u' and '0': the first yields plain uncompressed output whereas the latter outputs uncompressed data wrapped in the zlib format. @example rwb .. compressed BCF, BAM, FAI rwbu .. uncompressed BCF rwz .. compressed VCF rw .. uncompressed VCF